Comments (5)
Dear leonard-creator:
Can you send me a copy of the bam file, my email is [email protected]. So, I can run some tests and try to locate the errors.
Thanks
Hongyu Ding
from mamnet.
Dear leonard-creator:
I just updated the code; can you try the latest version and give me feedback?
Thanks
Hongyu Ding
from mamnet.
Hi Hongyu Ding,
I tryed again unfortunately still the same problem. Nothing happens after: 'Stop signal sended to callsv. Also, it doesn't matter what number of threads I enter as parameters, the actual threads are always much more. And the problem of the program not terminating fully is also still there.
python MAMnet.py -bamfilepath md_bam/HG00733.svision.demo.md.bam -workdir workdir/ -outputpath results/variants.vcf -step 50 -threads 2
python MAMnet.py -bamfilepath md_bam/HG00733.svision.demo.md.bam -workdir workdir/ -outputpath results/variants.vcf -step 50 -threads 12
![multiple_threads](https://private-user-images.githubusercontent.com/80115155/271936274-4486a66f-f712-400b-969b-ea1891cd9218.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.C3Umn0FfOw4QsoulBJQ9mlLgtnFgAD8CF9jV4CYM3uA)
from mamnet.
Dear leonard-creator:
I am still trying to reproduce the error, once I fixed I will let you know.
Thanks.
Hongyu Ding
from mamnet.
Hi Hongyu Ding,
I debugged myself and could identify the error in the call_sv function, which seems to have problems loading the model. I fear, something with my GPU-tensorflow combined settings is not right. I will investigate more and let you know as well.
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Related Issues (10)
- Any test data? HOT 1
- Segmentation fault HOT 3
- More specified dependency information HOT 2
- Failed to find any matching files for ./type HOT 3
- Is there any way to output REF and ALT sequence? HOT 2
- argument: -outputpath does not work as expected HOT 1
- Segmentation fault while running MAMnet with slurm HOT 1
- pyalign.py file HOT 3
- MD tags with Nanopore data HOT 3
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